Biology subjects

Wright, A.

Publications and source records attributed to Wright, A..

28 records · Page 2Linked to original sources

bioRxiv2023

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes

Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome, an open source, manually curated, peer-reviewed database of human biological pathways, provides annotations for over 4000 disease variants of close to 400 genes in the context of [~]800 disease reactions constituting [~]400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics (ACMG). Reactomes pathway-based, reaction-specific disease variant dataset and data model provide a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity.

systems biology↗

bioRxiv2023

Simulating atmospheric drought: Silica gel packets dehumidify mesocosm microclimates

O_LIAs global temperatures rise, droughts are becoming more frequent and severe. To predict how drought might affect plant communities, ecologists have traditionally designed experiments with controlled watering regimes and rainout shelters. Both treatments have proven effective for simulating soil drought. However, neither are designed to directly modify atmospheric drought. C_LIO_LIHere, we detail the efficacy of a silica gel atmospheric drought treatment in outdoor mesocosms with and without a cooccurring soil drought treatment. At California State University, Los Angeles, we monitored relative humidity (RH), temperature, and vapor pressure deficit (VPD) every 10 minutes for five months in a bare-ground experiment featuring mesocosms treated with soil drought (reduced watering) and/or atmospheric drought (silica packets suspended 12 cm above soil). C_LIO_LIWe found that silica packets dehumidified these microclimates most effectively (-5% RH) when combined with reduced soil water, regardless of the ambient humidity levels of the surrounding air. Further, packets increased microclimate VPD most effectively (+0.4 kPa) when combined with reduced soil water and ambient air temperatures above 20{degrees}C. Finally, packets simulated atmospheric drought most consistently when replaced within three days of deployment. C_LIO_LIOur results demonstrate the use of silica packets as effective dehumidification agents in outdoor drought experiments. We emphasize that incorporating atmospheric drought in existing soil drought experiments can improve our understandings of the ecological impacts of drought. C_LI

ecology↗

bioRxiv2023

Loss of NR2E3 disrupts rod photoreceptor cell maturation causing a fate switch late in human retinal development.

While dysfunction and death of light-detecting photoreceptor cells underlie most inherited retinal dystrophies, knowledge of the species-specific details of human rod and cone photoreceptor cell development remains limited. Here, we generate retinal organoids using induced pluripotent stem cells (iPSC) derived from a patient with genetic photoreceptor disease due to mutations in NR2E3, an isogenic control, and an unrelated control. Organoids were sampled using single-cell RNA sequencing across the developmental window encompassing photoreceptor specification, emergence, and maturation, up to 260 days of in vitro differentiation. Using single-cell transcriptomics data, we reconstruct the rod photoreceptor developmental lineage and identify a branchpoint in development unique to the disease state that gives rise to a divergent rod photoreceptor cell population. We show that the rod-specific transcription factor NR2E3 is required for the proper expression of genes involved in phototransduction, including expression of the light-sensitive protein rhodopsin, which is absent in divergent rods. NR2E3-null rods additionally misexpress several cone-specific phototransduction genes at both the transcript and protein level. Using joint multimodal single-cell sequencing on late-stage retinal organoids, we further identify specific putative regulatory sites where rod-specific factors act to steer rod and cone photoreceptor cell development. Importantly, these findings are strikingly different than those observed in rodent models of disease. Together, these data provide a roadmap of human photoreceptor development and leverage patient iPSCs to define the specific roles of rod transcription factors in photoreceptor cell emergence and maturation.

developmental biology↗

bioRxiv2022

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made towards identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N=N-R), found in diverse chemicals in both food and drugs. Surprisingly, the canonical azoR gene in Escherichia coli was dispensable for azo bond reduction. Instead, azo reductase activity was controlled by the fumarate and nitrate reduction (fnr) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of the fnr regulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical motifs found in both dietary and pharmaceutical compounds. IMPORTANCEThis work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and non-enzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen and cysteine, control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.

microbiology↗

bioRxiv2022

SexFindR: A computational workflow to identify young and old sex chromosomes

Sex chromosomes have evolved frequently across the tree of life, and have been a source of fascination for decades due to their unique evolutionary trajectories. They are hypothesised to be important drivers in a broad spectrum of biological processes and are the focus of a rich body of evolutionary theory. Whole-genome sequencing provides exciting opportunities to test these theories through contrasts between independently evolved sex chromosomes across the full spectrum of their evolutionary lifecycles. However, identifying sex chromosomes, particularly nascent ones, is challenging, often requiring specific combinations of methodologies. This is a major barrier to progress in the field and can result in discrepancies between studies that apply different approaches. Currently, no single pipeline exists to integrate data across these methods in a statistical framework to identify sex chromosomes at all ages and levels of sequence divergence. To address this, we present SexFindR, a comprehensive workflow to improve robustness and transparency in identifying sex-linked sequences. We validate our approach using publicly available data from five species that span the continuum of sex chromosome divergence, from homomorphic sex chromosomes with only a single SNP that determines sex, to heteromorphic sex chromosomes with extensive degeneration. Next, we apply SexFindR to our large-scale population genomics dataset for sea lamprey, a jawless vertebrate whose sex determination system remains a mystery despite decades of research. We decisively show that sea lamprey do not harbour sex-linked sequences in their somatic genome, leaving open the possibility that sex is determined environmentally or within the germline genome.

evolutionary biology↗

bioRxiv2021

Insecticide resistance characteristic of Anopheles vector species successfully controlled by deployment of pyrethroid and PBO long lasting insecticidal treated nets (LLINs) in Tanzania

Long lasting insecticidal nets (LLINs) are a proven tool to reduce malaria transmission, but in Africa efficacy is being reduced by pyrethroid resistance in the major vectors. A cluster randomized trial in Muleba district, Tanzania demonstrated that permethrin LLINs co-treated with piperonyl butoxide (PBO), a synergist that can block pyrethroid-metabolizing enzymes in the mosquito, had much greater efficacy than pyrethroid-only nets. Insecticide resistance profiles and underlying mechanisms were investigated in Anopheles gambiae and An. funestus from Muleba during the trial. Diagnostic dose bioassays using permethrin, together with intensity assays, suggest pyrethroid resistance that is both strong and very common, but not extreme. Transcriptomic analysis found multiple P450 genes over expressed including CYP6M2, CYP6Z3, CYP6P3, CYP6P4, CYP6AA1 and CYP9K1 in An. gambiae and CYP6N1, CYP6M7, CYP6M1 and CYP6Z3 in An. funestus. Indeed, very similar suites of P450 enzymes commonly associated with resistant populations elsewhere in Africa were detected as over expressed suggesting a convergence of mechanisms across Sub-Saharan African malaria vectors. The findings give insight into factors that may correlate with pyrethroid PBO LLIN success, broadly supporting model predictions, but revision to guidelines previously issued by the World Health Organization is warranted.

molecular biology↗

bioRxiv2020

SFPQ intron retention, reduced expression and aggregate formation in central nervous system tissue are pathological features of amyotrophic lateral sclerosis

BackgroundSplicing factor proline and glutamine rich (SFPQ, also known as polypyrimidine tract-binding protein-associated-splicing factor, PSF) is a RNA-DNA binding protein with roles in key cellular pathways such as DNA transcription and repair, RNA processing and paraspeckle formation. Dysregulation of SFPQ is emerging as a common pathological feature of multiple neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Increased retention of SFPQ intron nine and nuclear loss of the protein have been linked to multiple genetic subtypes of ALS. Consequently, SFPQ dysregulation has been hypothesised to be a common pathological feature of this highly heterogeneous disease. MethodsThis study provides a comprehensive assessment of SFPQ pathology in large ALS patient cohorts. SFPQ gene expression and intron nine retention were examined in multiple neuroanatomical regions and blood from ALS patients and control individuals using RNA sequencing (RNA-Seq) and quantitative PCR (RT-qPCR). SFPQ protein levels were assessed by immunoblotting of patient and control motor cortex and SFPQ expression pattern was examined by immunofluorescent staining of patient and control spinal cord sections. Finally, whole-genome sequencing data from a large cohort of sporadic ALS patients was analysed for genetic variation in SFPQ. ResultsSFPQ intron nine retention was significantly increased in ALS patient motor cortex. Total SFPQ mRNA expression was significantly downregulated in ALS patient motor cortex but not ALS patient blood, indicating tissue specific SFPQ dysregulation. At the protein level, nuclear expression of SFPQ in both control and patient spinal motor neurons was highly variable and nuclear depletion of SFPQ was not a consistent feature in our ALS cohort. However, we did observe SFPQ-positive cytoplasmic ubiquitinated protein aggregates in ALS spinal motor neurons. In addition, our genetic screen of ALS patients identified two novel, and two rare sequence variants in SFPQ not previously reported in ALS. ConclusionsThis study shows that dysregulation of SFPQ is a feature of ALS patient central nervous system tissue. These findings confirm SFPQ pathology as a feature of ALS and indicate that investigations into the functional consequences of this pathology will provide insight into the biology of ALS.

neuroscience↗

bioRxiv2019

Population coding of strategic variables during foraging in freely-moving macaques

Until now it has been difficult to examine the neural bases of foraging in naturalistic environments because previous approaches have relied on restrained animals performing trial-based foraging tasks. Here, we allowed unrestrained monkeys to freely interact with concurrent reward options while we wirelessly recorded population activity in dorsolateral prefrontal cortex (dlPFC). The animals decided when and where to forage, based on whether their prediction of reward was fulfilled or violated. This prediction was not solely based on a history of reward delivery, but also on the understanding that waiting longer improves the chance of reward. The decoded reward dynamics were continuously represented in a subspace of the high-dimensional population activity, and predicted animals subsequent choice better than the true experimental variables and as well as the raw neural activity. Our results indicate that monkeys foraging strategy is based on a cortical model of reward dynamics as animals freely explore their environment.

neuroscience↗

bioRxiv2019

Pneumococcal Colonisation is an Asymptomatic Event in Healthy Adults using an Experimental Human Colonisation Model.

IntroductionPneumococcal colonisation is regarded as a pre-requisite for developing pneumococcal disease. In children previous studies have reported colonisation to be a symptomatic event and described a relationship between symptom severity/frequency and colonisation density. The evidence for this in adults is lacking in the literature. This study uses an experimental human pneumococcal challenge model to explore whether pneumococcal colonisation (or co-colonisation with a respiratory virus) is a symptomatic event in healthy adults.\n\nMethodsHealthy volunteers aged 18-50 were recruited and inoculated intra-nasally with either Streptococcus pneumoniae (serotypes 6B, 23F) or saline as a control. Respiratory viral swabs were obtained prior to inoculation. Nasal and non-nasal symptoms were then assessed using a modified Likert score between 1 (no symptoms) to 7 (cannot function). The rate of symptoms reported between groups was compared and a correlation analysis performed.\n\nResultsData from 54 participants were analysed. 46 were inoculated with S. pneumoniae (29 with 6B, 17 with 23F) and 8 received saline. In total, 14 became experimentally colonised (30.4%), all of which were inoculated with 6B serotype. There was no statistically significant difference in nasal (p= 0.45) or non-nasal symptoms (p=0.28) between the pneumococcal inoculation group and the saline group. There was no direct correlation between colonisation density and symptom severity in those who were colonised. In the 22% (12/52) who were co-colonised with pneumococcus and respiratory viruses there was no statistical difference in either nasal or non-nasal symptoms (virus positive p=0.74 and virus negative p=1.0).\n\nConclusionPneumococcal colonisation is asymptomatic in healthy adults, regardless of bacterial density or viral co-colonisation.

microbiology↗

bioRxiv2017

Acetazolamide reduces exercise capacity following a five-day ascent to 4559 m on Monte Rosa

Acetazolamide (Az) is widely used to prevent and treat the symptoms of acute mountain sickness (AMS) but whether it alters exercise capacity at high altitude is unclear. Az (250 mg twice daily) or placebo were administered to 20 healthy adults (age range, 21-77 years) in a double-blind, randomized manner. Participants ascended over five days to 4559 m, before undertaking an incremental exercise test to exhaustion on a bicycle ergometer, with breath-by-breath gas measurements recorded using a portable gas analysis system. Maximum power output (Pmax) was reduced on Az compared with placebo (p=0.03), as was maximum O2 uptake (VO2max) (20.7 vs 24.6 mL/kg/min; p=0.06) and maximum expired CO2 (VCO2max) (23.4 vs 29.5 mL/kg/min; p=0.01). Comparing individuals matched for similar characteristics, Az-treated participants had smaller changes than placebo-treated participants in minute ventilation (88 vs 116 L/min: p=0.05), end tidal O2 (6.6 vs 9.3 mm Hg: p=0.009), end-tidal CO2 (-2.3 vs -4.2 mm Hg: p=0.005), VO2max (9.8 vs 13.8 mL/kg/min; p=0.04) and VCO2max (14.7 vs 20.8 mL/kg/min; p=0.009). There was a negative correlation between the mean ages of paired vs placebo-treated individuals and differences in Pmax reductions from base-line to altitude (r =-0.83: p<0.005) and HRmax at altitude (r=-0.71; p=0.01). Glomerular filtration rate (measured at sea-level) declined with increasing age (r=-0.69; p=0.001). Thus, 250mg of Az twice daily reduced exercise performance, particularly in older individuals. The age-related effects of Az may reflect higher tissue concentrations due to reduced drug clearance in older people.

physiology↗